Here are all the possibilities for two cubies with both faces misplaced in the locations that match the setup for Sequence 3C-E3 (additional misplaced facelets on the bottom face are not part of the setup and can be ignored). This shows that the sequence always fixes at least two misplaced facelets. This means that while solving a scrambled cube you do not have to match individual facelets to the setup, you only need to make sure that both facelets are misplaced on both edge pieces.